Michael Gove said they were "accelerating the pace of reform" and the review was needed because of the growth in academies.
Councils provide support services such as special needs education for state schools, but not academy schools.
Ministers had said the grant to provide such services would be cut by ?148m this year and ?265m next year.
In May, 23 councils threatened legal action saying the method used to calculate the cut breached guidelines.
'U-turn'Mr Gove told the BBC some Labour local authorities were "a bit unhappy" about the pace of reform, but "the truth is at the moment we're actually providing funding to local authorities and to schools for the same service".
The education secretary said they had to make sure the taxpayer "is not paying twice".
Labour says the decision shows changes are being pushed through too quickly.
"This is the third time in a year that Michael Gove has had to U-turn under the threat of legal action," shadow education secretary Andy Burnham said.
"And the reason that it keeps happening is that he is railroading his policies through without proper consultation, without listening to parents, to teachers, to local councillors."
'Hideously complicated'National Association of Head Teachers General Secretary Russell Hobby says funding formulas for schools are "hideously complicated".
"I think if we were charitable we'd be calling it a refinement of the policy here. The government's been moving at pace, in some cases rushing into things and I think then you find out that implementation is not as clear as you thought," he said.
"They've found that it's not as simple as cutting out the money that would have been spent on those schools when they become an academy."
But a spokesman for the Department of Education said it welcomed the opportunity to re-enter discussions with local authorities.
He said the need to review funding reflected the popularity of the academy programme.
According to the Department of Education website, 1,244 schools have applied to be an academy since June 2010 and 704 academies are in operation.
Reduced grantAcademies are outside of the local authority support structure, and receive no services from councils. Instead, they receive their funding directly from the government.
Once operating as an academy, the school receives the same per pupil funding as other state schools. However, it also gains control of a portion - up to 10% - of its budget which would previously have been held back by the local authority and used to provide services across the borough.
The Department for Education, through the local government settlement, said it was reducing the grant available to councils for support to schools to compensate for this.
The councils claim this cut has been calculated by deducting the amount it will cost individual academies to run those services themselves, rather than by the amount that councils will save by not providing them.
This, they argue, will leave them out of pocket and is against the government's own guidelines, known as the New Burdens Rules, on such matters.
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